[Chimera-users] Structure editing: add charge

George Tzotzos gtzotzos at me.com
Fri Apr 18 11:13:08 PDT 2014


Hi Elaine,

Thank you for the suggestion. I was not aware of the label opt / selattr options.

The charge of the octenoic acid was - 0.999, not +. My mistake and apologies for this.

Best wishes

George

On Apr 18, 2014, at 2:05 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi George,
> The calculation of charges for nonstandard residues is done by the Antechamber package included with Chimera, rather than Chimera directly.  I'm guessing that small (e.g. 0.001) deviations from integer total charges are fairly common and are caused by rounding of the per-atom values. 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html#antechamber>
> 
> I don't know of any way to prevent that (maybe the amber list people would have comments?), but once you see the total you can manually edit the charges, either in the output file (as you did) or directly in Chimera with the "setattr" command.  You would still have to decide which charges to adjust and how much to adjust them yourself, however, so I'm not sure if you would consider changing them in Chimera to be more intelligent.  It might be easier just to edit the output file.
> 
> Nevertheless, an example with neutral octenoic acid fetched from Pub3D.  Commands:
> 
> open pubchem:543977
> addcharge
> 
> ... this reports net charge 0.001.  So I show the charge values as labels and can change one or more, for example:
> 
> labelopt info charge
> label
> setattr a charge -.488 @o1
> label
> 
> But now I wonder why your octenoic acid charge was close to 1.  Shouldn't it be close to -1, or 0 if you are using the protonated form?
> 
> Sorry I don't have a better answer about enforcing integral charge. Wishing you a good weekend too,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Apr 18, 2014, at 4:28 AM, George Tzotzos wrote:
> 
>> In relation to my earlier message, I have found a fix (or, at least, I hope I have found one). I have manually edited the ligand.mol file to ensure an integer sum of charges. However, I would welcome any more intelligent way of doing the same.
>> 
>> Apologies for bothering you with this question.
>> 
>> A good weekend to you all
>> 
>> George
>> 
>> On Apr 18, 2014, at 8:03 AM, George Tzotzos <gtzotzos at me.com> wrote:
>> 
>>> Hi everybody,
>>> 
>>> I’m trying to add  to a ligand intended for an MD simulation using Amber. The ligand is 7-octenoic acid. The charge added to the ligand is non-integer 0.999.
>>> Given that he unperturbed charge on the protein is +9.000, the charge on the complex is +9.999. Amber does not accept non-integer charges, so it adds on 9 Na+ ions. 
>>> 
>>> Is there a way to force the charge on the ligand to be +1.000?
>>> 
>>> Apologies if this question should be addressed to the Amber list, but I used chimera to add hydrogens and charges (AM1-BCC). 
>>> 
>>> Regards
>>> George
> 




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